Hi, I'm sorry to hear about your horrible experience. We live in a world in which men think it is their right to commit violent acts against women, and it's so wrong. But there is one thing you don't need to worry about. Since your last period came more recently than the rape, and your ultrasounds line up with conception in mid-November, there is no risk that the rape produced the pregnancy. You hardly even would need a test, except for peace of mind.
If this is still troubling you after the doctor has told you when you conceived by all the medical evidence, it could be that the emotional effects of the assault are still with you, popping up as worries about paternity. (Women often write in to this forum whose worries or anxieties about something else have morphed into obsession that the wrong guy is the dad, not only in the case of rape but in other situations that involve strong emotion. Oddly, it's a form of wanting control over a situation in which they feel out of control.) But even if the rape might have long-reaching emotional effects, the actual sperm was entirely dead and gone, and could not affect you in any way, by the time you got pregnant. Is your rapist being prosecuted? Do you have counseling help? Addressing the lack of control, pain and anxiety of a rape seems important for a lot of reasons, and one is to prevent that stress from devolving into worries that somehow there is a question about paternity. There really isn't. So, don't worry about that, and if it's your boyfriend who is pushing the worry don't let him worry about it either.
Please take care.